FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: KRVK3
Calculation Name: 1L2Y-A-MD57-72800ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-13
Reference:
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | No |
| Water | No |
| Procedure | Manual calculation |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 10 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -24664.051008 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20061.80986 |
| FMO2-HF: Total energy | -4602.241148 |
| FMO2-MP2: Total energy | -4615.69844 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
"| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(:1:GLN )
Summations of interaction energy for
fragment #1(:1:GLN )
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| -123.197 | -111.078 | 18.173 | -14.044 | -16.249 | -0.149 |
Interaction energy analysis for fragmet #1(:1:GLN )
| frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 3 | GLN | 0 | 0.083 | 0.032 | 3.847 | -1.273 | 0.101 | -0.011 | -0.510 | -0.852 | -0.001 | |
| 4 | 4 | GLN | 0 | -0.015 | -0.009 | 5.489 | 1.600 | 1.600 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.030 | 0.024 | 6.332 | -3.283 | -3.283 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.020 | -0.012 | 2.129 | -10.158 | -8.276 | 1.331 | -1.085 | -2.128 | -0.003 | |
| 7 | 7 | GLN | 0 | 0.072 | 0.060 | 2.017 | -21.477 | -18.586 | 5.912 | -4.239 | -4.565 | -0.062 | |
| 8 | 8 | GLN | 0 | -0.035 | -0.038 | 2.147 | -33.912 | -31.259 | 9.616 | -6.054 | -6.215 | -0.052 | |
| 9 | 9 | GLN | 0 | -0.034 | -0.040 | 2.603 | -23.195 | -19.924 | 1.326 | -2.150 | -2.447 | -0.031 | |
| 10 | 10 | GLN | -1 | -0.862 | -0.899 | 5.067 | -31.499 | -31.451 | -0.001 | -0.006 | -0.042 | 0.000 |